Contacts of the strand formed by residues 43 - 50 (chain E) in PDB entry 4PHZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 43 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ARG 3.8 13.3 - - - +
42E THR* 1.3 90.0 + - - +
44E ASN* 1.3 65.1 + - - +
45E TRP* 3.8 25.2 + - + -
67E VAL* 3.5 18.8 - - + -
68E HIS 3.6 0.2 - - - -
69E VAL* 4.1 25.1 - - + -
73E TRP* 4.3 10.5 - - + -
80E PRO* 5.9 0.2 - - + -
112E LEU* 4.4 10.5 - - + -
138E ILE* 3.6 46.4 - - + -
140E VAL* 5.6 0.9 - - + -
146E ILE* 3.9 28.1 - - + +
321E ALA 4.4 2.6 - - - +
322E ALA* 5.4 0.2 - - - -
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Residues in contact with ASN 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET 3.2 20.5 - - - +
42E THR 4.7 0.7 - - - -
43E LEU* 1.3 76.3 - - - +
45E TRP* 1.3 62.6 + - - +
46E TYR* 3.8 5.4 - - - -
67E VAL* 3.2 4.7 - - - +
68E HIS* 2.7 59.7 + - + +
70E PHE* 3.4 29.5 - - - +
320E THR* 5.4 3.8 - - + +
321E ALA 3.7 12.1 - - - +
390E GLY* 3.8 19.8 - - - -
391E LEU* 4.0 19.9 - - + +
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Residues in contact with TRP 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.8 34.2 + - + +
44E ASN* 1.3 72.5 - - - +
46E TYR* 1.3 63.8 + - - +
48E VAL* 4.3 3.6 - - + -
66E LYS 3.7 4.3 - - - -
67E VAL* 3.8 13.0 - - + -
85E LEU* 5.7 0.7 - - + -
120E PHE* 3.8 35.4 - + - -
136E ALA* 3.9 17.0 - - + -
137E GLN 4.0 2.2 - - - -
138E ILE* 3.8 38.1 - - + -
146E ILE* 3.6 18.5 - - - +
147E ILE 3.6 7.9 + - - -
148E GLY* 3.3 32.4 - - - -
149E PRO* 3.7 23.4 - - + +
320E THR* 3.4 25.2 - - - +
322E ALA* 4.5 2.7 - - - -
323E GLY* 4.3 18.1 - - - +
391E LEU* 5.8 0.3 - - - +
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Residues in contact with TYR 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ASN 3.8 8.5 - - - -
45E TRP* 1.3 75.2 - - - +
47E ASP* 1.3 83.8 + - - +
48E VAL* 3.1 5.6 + - - +
65E GLY* 3.9 0.2 - - - -
66E LYS* 2.9 69.1 + - + +
67E VAL 3.8 11.2 - - - -
68E HIS 4.1 1.3 - - - -
117E ASP* 2.5 38.8 + - - +
271E ILE* 3.7 10.2 - - - +
276E THR* 4.3 9.8 + - - -
320E THR* 5.3 2.0 - - + +
325E ARG* 6.6 0.2 - - - +
391E LEU* 3.9 14.8 - - + -
393E PHE* 3.8 31.4 - + + -
401E ARG* 3.7 16.6 - - - -
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Residues in contact with ASP 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E TYR* 1.3 78.6 - - + +
48E VAL* 1.3 65.2 + - - +
49E GLN* 3.4 22.7 + - - +
64E SER* 3.6 0.9 + - - +
65E GLY* 3.5 11.2 - - - -
66E LYS* 2.6 38.1 + - + +
325E ARG* 6.1 4.1 - - - +
338E PHE* 5.9 1.2 - - - -
401E ARG* 2.7 44.9 + - - -
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Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E TRP* 4.3 11.7 - - + -
46E TYR* 4.0 11.0 - - - +
47E ASP* 1.3 78.3 - - - +
49E GLN* 1.3 67.1 + - - +
50E TRP* 3.4 34.5 - - + -
63E LEU* 3.6 17.0 - - + -
64E SER 3.2 5.4 - - - +
65E GLY* 4.1 0.2 - - - -
120E PHE* 4.5 15.9 - - + -
136E ALA* 4.8 3.6 - - + -
149E PRO* 3.7 37.5 - - + +
337E ASP 5.6 0.5 - - - +
338E PHE* 3.8 24.6 - - + -
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Residues in contact with GLN 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ASP* 3.9 21.6 + - - +
48E VAL* 1.3 78.3 - - - +
50E TRP* 1.3 71.3 + - - +
51E SER 3.9 1.1 - - - +
62E VAL 3.5 1.9 - - - +
63E LEU* 3.3 4.2 - - - +
64E SER* 2.8 51.3 + - - +
66E LYS* 6.1 0.2 - - - +
337E ASP 6.1 0.4 - - - +
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Residues in contact with TRP 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E VAL* 3.4 32.8 - - + -
49E GLN* 1.3 76.6 - - - +
51E SER* 1.3 68.2 + - - +
52E LYS* 2.9 20.3 + - - +
53E THR* 4.6 6.0 - - + +
61E MET* 3.8 17.5 - - + -
62E VAL 3.6 2.9 - - - -
63E LEU* 3.5 21.7 - - + +
134E VAL* 3.2 19.2 + - + -
149E PRO* 3.5 31.9 - - + -
150E GLY 3.6 4.3 - - - -
151E GLN* 3.3 26.8 - - + +
153E ILE* 3.8 16.4 - - + -
338E PHE* 4.4 2.2 - + - -
339E PRO* 3.6 35.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il